Human papillomavirus (HPV) is thought to be sexually transmitted; however, there have been a few studies investigating a possible iatrogenic source of infection.Therefore, it is important to assess the cleaning methods of reusable medical devices. This study assessed whether cleaning methods of flexible endoscopes in an otolaryngology clinic are effective against HPV. There were 24 patients with a history of head and neck cancer in the study; however, two outliers were excluded.Nine patients were confirmed to have HPV-associated cancer. PCR was used to measure and quantify the viral genomes of samples collected before and after cleaning. After cleaning, few HPV+ samples had endoscopes with less DNA than before cleaning. Additionally, for several patients with non-HPV-associated head and neck cancer, PCR showed more DNA after cleaning than before cleaning, suggesting residual HPV DNA within the cleaning solution. There was no significant difference (p > 0.05) between pre-and post-cleaning in both cohorts. Current cleaning methods of reusable endoscopes may not be effective in completely removing viral DNA.